tbuckley/cabot-search huggingface dataset:
DIPG-38. PATIENT-DERIVED THREE-DIMENSIONAL AVATARS REVEAL CELL-AUTONOMOUS MECHANISMS DRIVING INVASION AND METASTATIC PROGRESSION IN DIFFUSE MIDLINE GLIOMAS
Authors: Marco Bruschi, Lilia Midjek, Yassine Ajlil, Stephanie Vairy, Manon Lancien, Samia Ghermaoui, Thomas Kergrohen, Maïté Verreault, Ahmed Idbaih, Kévin Beccaria, Thomas Blauwblomme, Stéphanie Puget, Arnault Tauziede-Espariat, Pascale Varlet, Volodia Dangouloff-Ros, Nathalie Boddaert, Gwenael Le Teuff, Jacques Grill, Guillaume Montagnac, Nadia Elkhatib, Marie-Anne Debily, David Castel
Journal: Neuro-Oncology (2023)

Abstract Diffuse midline gliomas H3K27-altered are pediatric tumors associated with dismal survival after diagnosis that are characterized by their ability to infiltrate the entire central nervous system. We show that the extent of tumor invasion and metastatic progression represent critical adverse prognostic factors affecting the survival of DMG patients. Yet, no genetic alterations associate to the tumor progression patterns. We therefore used glioma stem cells collected at diagnosis to create patient-specific 3D avatars. We found that their invasive behaviour faithfully predicts metastatic relapse in patients, thus proving DMG spread is mainly an autonomous ability of tumor cells. This relevant modelling strategy revealed the existence of phenotypic entities associated with distinct migration modalities and capacities. Using transcriptomics of both organoids and primary tumors, we identified the biological programs associated with variable invasiveness. Importantly, we show that Bone Morphogenetic Protein 7 (BMP7) signalling is a crucial tumour-autonomous regulator of DMG invasiveness via the control of a phenotypic switch. We further deciphered effectors downstream of BMP7 stimulation as actionable targets to reduce invasion. These findings have two possible therapeutic applications. First, glioma stem cell 3D models represent a tool for tumor phenotypic stratification to rapidly predict patients with exacerbated invasiveness and increased risk of metastatic progression. This may allow to propose whole-brain or cranio-spinal irradiation within weeks after diagnosis to prevent the appearance of distant foci. Second, targeting autocrine and short-range BMP7-related signalling may become a useful adjunct to the current therapeutics, which are mainly directed to control the disease locally.
BIOL-21. PATIENT-DERIVED, THREE-DIMENSIONAL ORGANOID PLATFORM FOR PEDIATRIC BRAIN TUMOR MODELING AND THERAPEUTIC TESTING
Authors: David Beale, Valerie Baubet, Peeyush Goel, Luke Patterson, Fadi Jacob, Maria-Rita Santi-vicini, Angela Viaene, Guo-li Ming, Hongjun Song, Peter Madsen, Jessica Foster, Crystal Griffin, Ally Stern, Phillip Storm, Mateusz Koptyra, Adam Resnick
Journal: Neuro-Oncology (2023)

Abstract Brain tumors are the leading cause of cancer-related death in children. An important hurdle to scientific and clinical progress in the field has been the limited availability of preclinical tumor models. In recent years, the Children’s Brain Tumor Network (CBTN) has accelerated the development of patient-derived cell lines and xenografts, offering these resources to the community through open-source access. While these models are extremely valuable, their development process can be lengthy and result in clonally selected lines which presents a challenge for studying complex tumor biology. To address the need for three-dimensional tissue culture, our group in conjunction with CBTN, generates organoids from fresh tissue specimens obtained directly from surgical resection. This effort resulted in numerous organoid models generated for high-grade glioma (HGG), medulloblastoma, ependymoma, atypical teratoid-rhabdoid tumor, and low-grade glioma tumors. The tissue was processed within an hour post-extraction and cultured in growth factor-free media. Organoid formation and growth were observed as early as in 2 weeks post initiation and continued for up to three months. Banked organoids established growth upon return to culture and resembled similar cell composition to those in the original culture. This provides an excellent preclinical testing model for precision medicine-driven trials. To represent this, we utilized CAR-T testing approach and treated GD2-positive HGG organoids with GD2 CAR-T cells and control CD19 CAR-T cells. 72h exposure to GD2 CAR-T induced morphological changes and significant increase in dead cells within organoids, which was not observed in CD19 CAR-T treated counterparts (p&amp;lt;0.05). Here we provide a simple and efficient workflow for the generation and testing of three-dimensional tumor organoid models generated from fresh surgical tissue. The platform can accelerate not only tumor biology explorations but also empower a diverse array of precision medicine-driven testing for pediatric brain tumors.
TRLS-16. RAPID GENERATION OF EPENDYMOMA MOUSE MODELS FOR PRE-CLINICAL STUDIES
Authors: Siri Ippagunta, Erik Emanus, Kelsey Bertrand, Stephen Mack
Journal: Neuro-Oncology (2023)

Abstract Pediatric Ependymomas are the leading cause of cancer death among children &amp; adolescents with the 5-year progression free survival (PFS)rate being &amp;lt; 30%. Despite this poor prognosis there has been less success in development of targeted therapies. A major drawback in developing new therapeutics is lack of proper models of disease. Objective of out work has been to develop orthogonal models of various distinct groups of ependymoma to enable understanding of tumor microenvironment thus leading to strategies targeting potential therapeutic sites. In this regard we have developed two models of ZFTA-RELA Ependymoma: 1) In Utero Electroporation Model: DNA plasmids are transfected into developing forebrain, 2) Allograft Model: Primary tumor derived or in vitro transducer cells are allografted into various regions of brain. Further we have shown that these models molecularly resemble patient-derived tumors using RNA sequencing. Using these ZFTA-RELA mouse models we have shown that NSG mice (n=8/treatment group) treated with Selinexor (an XPO1 inhibitor) in combination with chemotherapy have lower tumor volumes by 40% as compared to vehicle or chemotherapy alone treated mice (P&amp;lt;0.05). Furthermore the combination therapy treated mice have improved survival by 28 days as compared to vehicle mice. In conclusion, we have shown that our novel models of ependymomas not only closely resemble disease in patients, but can also be used to develop effective targeted therapies.
IMMU-18. TARGETING GD2 IN THALAMIC DIFFUSE MIDLINE GLIOMA WITH TRANSIENT MRNA CAR T CELLS
Authors: Jessica Foster, Peter Madsen, Kyra Harvey, Luke Patterson, Crystal Griffin, Allison Stern, Phillip Storm, Adam Resnick
Journal: Neuro-Oncology (2023)

Abstract Chimeric antigen receptor (CAR) T cells targeting the disialoganglioside GD2 have shown promise as a therapeutic for diffuse midline glioma (DMG). However, thalamic tumors have been excluded from clinical trials due to prior studies showing neurotoxicity and fatality when using virally transduced CAR T cells. We hypothesized repeated dosing of transient GD2-directed mRNA CAR T cells could be employed for safe and effective treatment of thalamic DMG. GD2-directed CAR T cells were created using mRNA and first tested against the murine thalamic DMG xenograft 7316-6349 via locoregional delivery with an indwelling catheter for repeated dosing. The previously reported fatal neurotoxicity observed in mice using lentiviral CAR T cells could be recapitulated with aggressive dosing. Four doses of 5x106 mRNA CAR T cells delivered intratumorally twice a week resulted in median overall survival of 9 days for GD2-treated mice compared to &amp;gt;30 days for CD19-treated controls (p&amp;lt;0.01). This toxicity could be avoided by decreasing the dose and timing of infusions to 2x106 mRNA CAR T cells delivered once weekly. Bioluminescent imaging showed regression of tumor in GD2-treated mice compared to CD19-treated controls (radiance fold change -3x106 versus +20x106 p/sec/cm2/sr, p&amp;lt;0.01). To assess survival before the onset of graft-versus-host disease, we utilized the aggressive hypermutant thalamic DMG model 7316-3058, treating with 2x106 CAR T cells intratumorally once weekly. Overall survival was significantly prolonged for 7316-3058 mice treated with GD2-directed mRNA CAR T cells compared to CD19-directed controls (median OS 48 days versus 33 days, p=0.03). Notably, non-tumor bearing mice treated with GD2-directed CAR T cells developed fatal neurotoxicity within 14 days, suggesting a very narrow therapeutic window in the brain. These data highlight the utility of titratable mRNA-based CAR T cell therapy for CNS tumors and establish GD2-directed mRNA CAR T cells as a safe and effective method for treating thalamic DMG.
Prenatal and Childhood Exposure to Organophosphate Pesticides and Behavior Problems in Adolescents and Young Adults in the CHAMACOS Study
Authors: Sharon K. Sagiv, Ana M. Mora, Stephen Rauch, Katherine R. Kogut, Carly Hyland, Robert B. Gunier, Asa Bradman, Julianna Deardorff, Brenda Eskenazi
Journal: Environmental Health Perspectives (2023)

Background: We previously reported associations of prenatal exposure to organophosphate (OP) pesticides with poorer neurodevelopment in early childhood and at school age, including poorer cognitive function and more behavioral problems, in the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS), a birth cohort study in an agriculture community. Objective: We investigated the extent to which early-life exposure to OP pesticides is associated with behavioral problems, including mental health, in youth during adolescence and early adulthood. Methods: We measured urinary dialkylphosphates (DAPs), nonspecific OP metabolites, in urine samples collected from mothers twice during pregnancy (13 and 26 wk) and at five different times in their children (ages 6 months to 5 y). We assessed maternal report and youth report of externalizing and internalizing behavior problems using the Behavior Assessment System for Children, 2nd edition (BASC-2), when the youth were ages 14, 16, and 18 y. Because there was evidence of nonlinearity, we estimated associations across quartiles of DAPs and modeled repeated outcome measures using generalized estimating equations. Results: There were 335 youths with prenatal maternal DAP measures and 14-. 16-, or 18-y BASC-2 scores. Prenatal maternal DAP concentrations (specific gravity–adjusted median, Q1–Q3=159.4, 78.7–350.4 nmol/L) were associated with higher T-scores (more behavior problems) from maternal report, including more hyperactivity [fourth vs. first quartile of exposure β=2.32; 95% confidence interval (CI): 0.18, 4.45], aggression (β=1.90; 95% CI: 0.15, 3.66), attention problems (β=2.78; 95% CI: 0.26, 5.30), and depression (β=2.66; 95% CI: 0.08, 5.24). Associations with youth report of externalizing problems were null, and associations with depression were suggestive (fourth vs. first quartile of exposure β=2.15; 95% CI: −0.36, 4.67). Childhood DAP metabolites were not associated with behavioral problems. Discussion: We found associations of prenatal, but not childhood, urinary DAP concentrations with adolescent/young adult externalizing and internalizing behavior problems. These findings are consistent with prior associations we have reported with neurodevelopmental outcomes measured earlier in childhood in CHAMACOS participants and suggests that prenatal exposure to OP pesticides may have lasting effects on the behavioral health of youth as they mature into adulthood, including their mental health. https://doi.org/10.1289/EHP11380
DIPG-19. BAF COMPLEX PERTURBATION AS A NOVEL THERAPEUTIC OPPORTUNITY IN H3K27M PEDIATRIC GLIOMA
Authors: Eshini Panditharatna, Joana G Marques, Tingjian Wang, Maria Trissal, Ilon Liu, Li Jiang, Alexander Beck, Andrew Groves, Neekesh Dharia, Samantha Hoffman, Guillaume Kugener, McKenzie Shaw, Olivia Hack, Joshua Dempster, Caleb Lareau, Michael Quezada, Ann-Catherine Stanton, Meghan Wyatt, Zohra Kalani, Amy Goodale, Francisca Vazquez, Federica Piccioni, John Doench, David Root, Jamie Anastas, Kristen Jones, Amy Conway, Sylwia Stopka, Michael Regan, Yu Liang, Hyuk-Soo Seo, Kijun Song, Puspalata Bashyal, Nathan Mathewson, Sirano Dhe-Paganon, Mario L Suvà, Angel M Carcaboso, Cinzia Lavarino, Jaume Mora, Quang-De Nguyen, Keith L Ligon, Yang Shi, Sameer Agnihotri, Nathalie Y R Agar, Kimberly Stegmaier, Charles D Stiles, Michelle Monje, Todd R Golub, Jun Qi, Mariella G Filbin
Journal: Neuro-Oncology (2023)

Abstract Epigenetic dysregulation resulting in stalled development plays a crucial role in pediatric cancer tumorigenesis. Diffuse midline gliomas (DMG) are universally fatal pediatric brain cancers refractory to standard of care treatment modalities. These malignancies are driven by heterozygous mutations in genes encoding histone 3 (H3K27M) which create an aberrant epigenetic landscape that keeps glioma cells in an undifferentiated stem-like state. Consequently, targeting epigenetic regulators to restore the epigenome and force glioma cells to exit this stem-like cell state represents a promising new therapeutic strategy for H3K27M-DMG. To interrogate for epigenetic dependencies, we performed a CRISPR/Cas9 inactivation screen in patient-derived H3K27M-DMG neurospheres using an epigenetically focused sgRNA library and identified several core components of the mammalian BAF (SWI/SNF) chromatin remodeling complex as genetic vulnerabilities. Validation assays revealed that knockout of the BAF catalytic subunit BRG1 results in decreased glioma cell proliferation and tumor growth in orthotopic mouse models. Mechanistically, genome wide localization and DNA accessibility studies combined with regulatory network analysis demonstrated that BRG1 controls the transcription factor and enhancer landscapes that maintain H3K27M-DMG cells in a cycling, oligodendrocyte precursor cell-like state. Single cell transcriptome analysis in vitro and immunofluorescence studies in vivo confirmed that genetic perturbation of this chromatin remodeler promotes progression of differentiation along the astrocytic lineage. Similarly, pharmacological suppression of BRG1 activity, using both catalytic inhibitors as well as recently developed degraders, opposes tumor cell proliferation, stimulates cell state transition, and improves overall survival of patient-derived xenograft models. Interestingly, these effects seem to be restricted to H3K27M mutant glioma, as H3 wildtype glioma cells were less sensitive to BRG1 inhibition both in vitro and in vivo. In summary, we demonstrate that the BAF complex contributes to the maintenance of glioma cells in a proliferative stem-like state and that its therapeutic inhibition has translational potential for children bearing H3K27M-DMG.
HGG-20. NOVEL PAEDIATRIC CASE OF A SPINAL HIGH-GRADE ASTROCYTOMA WITH PILOID FEATURES IN A PATIENT WITH NOONAN SYNDROME
Authors: Jordan Staunton, Pamela Ajuyah Robertson, Angela Harris, Chelsea Mayoh, Marie Wong, Megan Rumford, Noemi Fuentes-Bolanos, Mark Cowley, Loretta Lau, David S Ziegler, Paulette Barahona, Neevika Manoharan
Journal: Neuro-Oncology (2023)

Abstract Noonan Syndrome (NS) is a genetic condition, known to be associated with low grade central nervous system tumours in children but only very rarely associated with high-grade gliomas. Here we describe the first reported case of a spinal high-grade astrocytoma with piloid features (HGAP) in a child with NS. This case presented as a diagnostic and treatment dilemma, prior to comprehensive molecular profiling with whole-genome germline and tumour sequencing, tumour transcriptome sequencing and DNA methylation analysis. The methylation profile was a strong match for HGAP and was critical to establish this child’s diagnosis, as this is an essential diagnostic criteria for confirmation of this relatively new tumour group. Sequencing results identified activation of the MAPK signalling pathway with somatic variants in FGFR1 and NF1 and the previously known germline pathogenic variant in PTPN11. The somatic molecular profile was consistent with those previously reported in other HGAP case series and reports, whereas the germline finding has not been previously described in individuals with this tumour type. This patient’s molecular profile adds to the small group of paediatric cases reported in the literature, continuing to expand our understanding of this new WHO diagnostic category. Confirmation of this rare diagnosis was critical to this child’s management and targetable aberrations were identified, providing alternative therapeutic options. The therapeutic targets included known drivers within the MAPK pathway, but also changes not previously associated with HGAP such as differential expression of VEGFA and PD-L1. Together this case underscores the power of precision medicine from a diagnostic, therapeutic and clinical management perspective, and describes an association between HGAP and NS which has not previously been reported.
LGG-16. NOVEL COMBINATION THERAPIES FOR PEDIATRIC LOW-GRADE GLIOMA AND CHARACTERIZATION OF THE UNDERLYING CELL DEATH MECHANISMS
Authors: Constantia Zeiser, Lisa Rösch, Sonja Herter, Heike Peterziel, Florian Selt, Till Milde, Olaf Witt, Ina Oehme
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND The majority of pediatric low-grade gliomas (pLGGs) harbor a MAPK/ERK pathway overactivating alteration, making them suitable for MAPK-targeted therapies such as MEK inhibition. However, MEK inhibitor treatment alone is in most cases not sufficient to induce complete response, and a rapid rebound of the tumor is the consequence after withdrawal of the therapy. METHODS To identify novel cytotoxic drug combinations, we screened 89 clinically relevant drugs in combination with the MEK inhibitors trametinib and binimetinib. We assessed the regression of cultured 3D microtumors of patient-derived BT40 and BT314 cells, both harboring a BRAFV600E mutation. Depending on the inducible expression of SV40 large T antigen, the BT314 model can reflect two states, proliferation and oncogene-induced senescence. The area of spheroids was measured both in brightfield and with the fluorescent dye TMRE (mitochondrial polarization) at the start and the end of the treatment (6 days). Moreover, metabolic activity was determined through bulk ATP measurement. Drug hit combinations were further analyzed for the successful induction of cell death using high-content microscopy (HCM) imaging and enzymatic caspase activity assays. The microscopic readouts included Hoechst 33342 for the detection of nuclear morphology, BODIPY for sensitizing lipid peroxidation and CM-H2DCFDA as a general oxidative stress indicator. The images were analyzed with the automated image analysis program CellProfiler and the machine learning application CellProfiler Analyst. RESULTS The screening identified the following drug hits: navitoclax (BCL-2 family inhibitor), BRAF inhibitor dabrafenib, mTOR inhibitor everolimus and selinexor, a selective inhibitor of nuclear export. All drugs increased apoptotic cell death and ROS levels at clinically achievable drug concentrations, except the mTOR inhibitors. These results are currently validated in vivo with BT40 zebrafish embryo xenograft models. CONCLUSION Combinations of MEK inhibitors with navitoclax, dabrafenib or selinexor resulted in sufficient apoptosis to induce regression of pLGG microtumors in vitro.
IMMU-16. IDENTIFICATION OF TUMOR REJECTION ANTIGENS FOR PRECISION ADOPTIVE CELLULAR THERAPY FOR PEDIATRIC GLIOMAS
Authors: Vrunda Trivedi, Changlin Yang, Elizabeth Ogando-Rivas, Kyle Dyson, Duane Mitchell
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Identifying tumor rejection antigens remains a major barrier to developing effective antigen-directed immunotherapeutics and their application to pediatric brain tumors. Recent progress in the field of cancer immunogenomics has facilitated the search for tumor-specific antigens by applying comprehensive cancer genomics to tumor antigen discovery. Using a custom antigen prediction pipeline, we performed in silico antigen prediction across a broad array of antigen classes including neoantigens, tumor-associated antigens (TAAs), and fusion proteins for human and murine medulloblastoma tumors. We generated antigen-specific T-cells and validated the antigen-mediated immune responses for the development of precision adoptive cellular therapy. METHODS We evaluated WES and RNA-seq data from 170 medulloblastoma patients available through ICGC and performed a comprehensive immunogenomic analysis of subgroup-specific transcription profiles to identify candidate antigen targets. Antigen-specific T-cells were generated from healthy donor PBMCs stimulated against commonly recurring neoantigens and TAAs and immune response was evaluated using IFNγ secretion. Furthermore, we performed tumor antigen discovery for preclinical medulloblastoma models Ptch1 (sonic hedgehog driven) and NSC (Group 3 MYC-driven) and validated the antigen-mediated immune responses of ex vivo expanded antigen-specific T-cells. RESULTS Antigen prediction analysis revealed most tumors expressed a higher proportion of immunogenic TAAs than neoantigens and fusion proteins. The neoantigens and TAAs evaluated in this study showed significantly higher IFN-γ secretion in an antigen-dependent manner for both the human and murine platform validation. We thus confirmed the capability to produce functional tumor antigen-specific T-cells that can be leveraged into adoptive cellular therapy for the treatment of medulloblastoma. CONCLUSION Medulloblastomas are immunologically heterogeneous, and identifying potential tumor rejection antigens is desirable to develop personalized immunotherapies for the patients. Using a custom antigen prediction and ex vivo antigen-specific T-cell expansion pipeline, we identified potential tumor rejection antigens with important implications for the development of antigen-directed cellular therapies.
TRLS-04. PRECLINICAL VALIDATION OF A NOVEL THERAPEUTIC STRATEGY FOR CHOROID PLEXUS CARCINOMA
Authors: Brice Martin, Tyler Garman, Madeline Laramee, Amy Wang, Xiaohu Zhang, Erin Beck, Kelli Wilson, Carleen Klumpp-thomas, Crystal Mcknight, Xin Xu, Natalie Hagen, David Holland, Craig Thomas, Nadia Thomas, Mark Souweidane
Journal: Neuro-Oncology (2023)

Abstract Choroid plexus carcinoma is a very rare pediatric tumor located in the fourth and lateral ventricles of the brain. It is known to have a severe clinical history and significant side effects because of intensive and noxious chemotherapies. Due to the disease’s rarity and the scarcity of biologically relevant substrates, the advance of new therapeutical techniques for this condition has been exceedingly constrained. A human patient-derived CPC cell line (CCHE-45, Children Cancer Hospital Egypt) was subjected to a high-throughput screen (HTS); 427 top hits were identified, highlighting critical molecular targets in CPC. Additionally, a combination screen with numerous different targets identified synergistic combinations that lead the way for brand-new CPC therapies. Based on in vitro efficiency, CNS penetrance ability and feasible translational potential, two combinations using a DNA alkylating or topoisomerase inhibitors in combination with an ataxia telangiectasia mutated and rad3 (ATR) inhibitor (topotecan/elimusertib and melphalan/elimusertib respectively) were validated in vitro and in vivo. Pharmacokinetic studies revealed greater CNS penetrance via intra-arterial (IA) delivery compared to intravenous (IV) delivery, as well as increased CNS penetrance for melphalan/elimusertib combination. Transcriptome analysis was used to evaluate the mechanisms of melphalan/elimusertib synergistic effect; deregulation of several carcinogenic pathways (e.g. MYC, mTOR, p53) as well as the activation of vital biological processes were revealed (e.g. DNA repair, apoptosis, hypoxia, interferon gamma). In a CPC genetic mouse model, IA administration of melphalan and elimusertib significantly increased survival. To the best of our knowledge, this work is the first using human CPC cells to identify several prospective combinatorial treatments and it highlights the effectiveness of IA delivery for the treatment of CPC.